The fundamental mystery of development is how a single fertilized egg cell multiplies and differentiates into a complex animal composed of a large number and wide variety of specialized organs, tissues, and cell types. Identification of the genes with the most pronounced effects on development is merely a first step to an understanding of the process. The second challenge is to understand how the activity of these genes unfolds in time and space to control the formation and patterning of animal body plans and body parts. This process is primarily a matter of gene regulation.
Every feature of animal development depends on both serial and parallel gene functions that act within and between regulatory hierarchies. Because evolutionary changes in animal development can arise from changes in the operation of regulatory hierarchies, understanding the genetic logic and molecular circuitry of major regulatory programs is fundamental to understanding the evolution of morphology.
In this chapter, we examine the architecture of developmental regulatory hierarchies at two levels. First, we analyze the genetic logic of the hierarchies that control the formation and patterning of the primary embryonic axes, appendages, organs, and other major features of selected model animals. Second, we analyze the ways in which combinations of regulatory inputs within these hierarchies are integrated at a molecular level by regulatory elements of developmental genes to control their stage- and tissue-specific expression and functions.
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